[gmx-users] Definiting protonation in pdb2gmx input

[mhuhtala at abo.fi]

One of the recurring questions on the list seems to be how to define  
residue protonation states non-interactively in pdb2gmx input. The  
interactive options are a bit of a nightmare to use. Could pdb2gmx be  
modified to optionally read the residue types from the PDB file  
itself? The user would replace e.g. "ASP " with "ASPH" in the PDB  
file, and pdb2gmx would build a protonated aspartate, whether the  
hydrogen atom is there in the PDB file or not. Same for all residue  
types, of course. The upside would be having readable and more easily  
scriptable input instead of trying to script the interactive input. I  
realize that the names of the residue types differ between force  
fields, but even requiring force field specific names would be ok as  
far as I'm concerned (ASPH in Gromos, ASH in Amber, etc.).